Bacteriophages pp 231-238 | Cite as

Phage Genome Annotation Using the RAST Pipeline

  • Katelyn McNair
  • Ramy Karam Aziz
  • Gordon D. Pusch
  • Ross Overbeek
  • Bas E. Dutilh
  • Robert Edwards
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1681)

Abstract

Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis. We provide a road map through the phage genome annotation pipeline, and discuss the challenges and solutions for phage genome annotation as we have implemented in the rapid annotation using subsystems (RAST) pipeline.

Key words

Phage Genome annotation RAST Functional annotation Gene predictions 

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Katelyn McNair
    • 1
  • Ramy Karam Aziz
    • 2
    • 3
  • Gordon D. Pusch
    • 3
  • Ross Overbeek
    • 3
  • Bas E. Dutilh
    • 4
    • 5
  • Robert Edwards
    • 1
    • 6
  1. 1.Computational Sciences Research CenterSan Diego State UniversitySan DiegoUSA
  2. 2.Department of Microbiology and Immunology, Faculty of PharmacyCairo UniversityCairoEgypt
  3. 3.Argonne National LaboratoryArgonneUSA
  4. 4.Theoretical Biology and BioinformaticsUtrecht UniversityUtrechtThe Netherlands
  5. 5.Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life SciencesRadboud University Medical CentreNijmegenThe Netherlands
  6. 6.Departments of Biology and Computer ScienceSan Diego State UniversitySan DiegoUSA

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